SNP Explorations

1) Search HapMap for the gene SCN5A, and click on one of the red diamonds to see what gene this is and the variability among the populations. What does this gene encode?

2) At the bottom, you see two alternative splicing cartoons that illustrate the two slight variants of this protein which differ by only one amino acid. Can you see the difference in the splicing for one amino acid?

3) Click on the splicing cartoon to read the summary since you cannot see the difference in the cartoon. At the top right of this page, click on the “Links” text and choose “Geneview in dbSNP” to see all the SNPs for this gene. Scroll down to find the mutation in codon 1102, which can lead to cardiac arrhythmia and is more prevalent in people of African descent. What is the rs# for this potentially lethal SNP?

4) Return to the HapMap view of SCN5A and try to find the rs# for the lethal mutation. This discovery question was designed to show that despite the vast amounts of information, there are still important gaps.

5) Search the Ensembl Human Genome Browser for SCN5A, follow the gene link and select SNP classification and coding variation from the various options to see Ensembl’s method for displaying SNP information. Do you find this display more or less helpful than NCBI’s?

6) Search Genewindow for SCN5A and consider this visualization. Click on the line showing the gene below the splicing cartoon and click near the middle of the gene. Navigate until you see exon 18. Can you find the cardiac arrhythmia SNP (converting Ser 1102 to Tyr) in this view? To help you find it, use the "annotations" menu on the left side, and select "variations" (be sure to allow popup windows in your browser). Scroll down to amino acid 1103 and click on the "goto" link in the left column this table. These directions should substantially improve your ability to see the lethal SNP.

© Copyright 2005. Malcolm Campbell. Department of Biology, Davidson College, Davidson, NC 28035
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